## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: VST

TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1    ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1    ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1    ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF17 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF30 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1   ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       1   ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15:       1   ORF53 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17:       1   ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18:       1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20:       1   ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 23:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 24:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 25:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2    ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       2   ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33:       2   ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34:       2   ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36:       2   ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43:       2   ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46:       2   ORF41 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49:       2   ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50:       2   ORF48 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51:       2   ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52:       2   ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53:       2   ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54:       2   ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55:       2   ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 56:       2   ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 57:       2   ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 58:       2   ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 59:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 60:       3    ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61:       3   ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62:       3   ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63:       3   ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64:       3   ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65:       3   ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66:       3   ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67:       3   ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68:       3   ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69:       3   ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 70:       3   ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 71:       3   ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 72:       3  NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 73:       3   ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 74:       4   ORF19 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 75:       4   ORF37 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 76:       4   ORF51 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 77:       4   ORF55 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 78:       4 ORF66_1 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 79:       5 ORF64_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.59026662
##  2: 0.002173813 -2.3786533 0.5530091 0.59026662
##  3: 0.002173813 -2.3786533 0.5530091 0.59026662
##  4: 0.002173813 -2.3786533 0.5530091 0.59026662
##  5: 0.002173813 -2.3786533 0.5530091 0.59026662
##  6: 0.002173813 -2.3786533 0.5530091 0.59026662
##  7: 0.002173813 -2.3786533 0.5530091 0.59026662
##  8: 0.002173813 -2.3786533 0.5530091 0.59026662
##  9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002173813 -2.3786533 0.5530091 0.59026662
## 23: 0.002173813 -2.3786533 0.5530091 0.59026662
## 24: 0.002173813 -2.3786533 0.5530091 0.59026662
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.002630562 -1.9748104 0.3778197 0.20208360
## 56: 0.002630562 -1.9748104 0.3778197 0.20208360
## 57: 0.002630562 -1.9748104 0.3778197 0.20208360
## 58: 0.002630562 -1.9748104 0.3778197 0.20208360
## 59: 0.002630562 -1.9748104 0.3778197 0.20208360
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005127433 -0.5566122 0.2345080 0.82739367
## 70: 0.005127433 -0.5566122 0.2345080 0.82739367
## 71: 0.005127433 -0.5566122 0.2345080 0.82739367
## 72: 0.005127433 -0.5566122 0.2345080 0.82739367
## 73: 0.005127433 -0.5566122 0.2345080 0.82739367
## 74: 0.005224449 -1.2350532 1.5108478 0.06845455
## 75: 0.005224449 -1.2350532 1.5108478 0.06845455
## 76: 0.005224449 -1.2350532 1.5108478 0.06845455
## 77: 0.005224449 -1.2350532 1.5108478 0.06845455
## 78: 0.005224449 -1.2350532 1.5108478 0.06845455
## 79: 0.002585386 -1.9080987 0.3087534 0.43210279
##           se.bp          v         c       pchi

## [1] "ORF74" "ORF41"
## [1] 2
##  [1] "ORF7"   "ORF24"  "ORF27"  "ORF28"  "ORF32"  "ORF35"  "ORF44"  "ORF45" 
##  [9] "ORF49"  "ORF56"  "ORF57"  "ORF59"  "NOIR_1" "ORF76"
## [1] 14

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1    ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1    ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1    ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       1   ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15:       1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17:       1   ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24:       2    ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2   ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2   ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       2   ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33:       2   ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40:       2   ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43:       2   ORF41 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46:       2   ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47:       2   ORF48 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48:       2   ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49:       2   ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50:       2   ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51:       2   ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52:       2   ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53:       2   ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54:       2   ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55:       2   ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 56:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 57:       3    ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 58:       3   ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 59:       3   ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 60:       3   ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61:       3   ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62:       3   ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63:       3   ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64:       3   ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65:       3   ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66:       3   ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67:       3   ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68:       3   ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69:       3  NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 70:       3   ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 71:       4   ORF17 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 72:       4   ORF30 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 73:       4   ORF53 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 74:       5   ORF19 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 75:       5   ORF37 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 76:       5   ORF51 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 77:       5   ORF55 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 78:       5 ORF66_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 79:       6 ORF64_1 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.59026662
##  2: 0.002173813 -2.3786533 0.5530091 0.59026662
##  3: 0.002173813 -2.3786533 0.5530091 0.59026662
##  4: 0.002173813 -2.3786533 0.5530091 0.59026662
##  5: 0.002173813 -2.3786533 0.5530091 0.59026662
##  6: 0.002173813 -2.3786533 0.5530091 0.59026662
##  7: 0.002173813 -2.3786533 0.5530091 0.59026662
##  8: 0.002173813 -2.3786533 0.5530091 0.59026662
##  9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002630562 -1.9748104 0.3778197 0.20208360
## 23: 0.002630562 -1.9748104 0.3778197 0.20208360
## 24: 0.002630562 -1.9748104 0.3778197 0.20208360
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.002630562 -1.9748104 0.3778197 0.20208360
## 56: 0.002630562 -1.9748104 0.3778197 0.20208360
## 57: 0.005127433 -0.5566122 0.2345080 0.82739367
## 58: 0.005127433 -0.5566122 0.2345080 0.82739367
## 59: 0.005127433 -0.5566122 0.2345080 0.82739367
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005127433 -0.5566122 0.2345080 0.82739367
## 70: 0.005127433 -0.5566122 0.2345080 0.82739367
## 71: 0.005224449 -1.2350532 1.5108478 0.06845455
## 72: 0.005224449 -1.2350532 1.5108478 0.06845455
## 73: 0.005224449 -1.2350532 1.5108478 0.06845455
## 74: 0.002585386 -1.9080987 0.3087534 0.43210279
## 75: 0.002585386 -1.9080987 0.3087534 0.43210279
## 76: 0.002585386 -1.9080987 0.3087534 0.43210279
## 77: 0.002585386 -1.9080987 0.3087534 0.43210279
## 78: 0.002585386 -1.9080987 0.3087534 0.43210279
## 79: 0.004830169 -0.9381876 0.3682901 0.16904056
##           se.bp          v         c       pchi

## [1] "ORF63" "ORF74" "CTO"   "ORF41"
## [1] 4
##  [1] "ORF7"    "ORF24"   "ORF27"   "ORF28"   "ORF32"   "ORF35"   "ORF44"  
##  [8] "ORF45"   "ORF49"   "ORF56"   "ORF57"   "ORF59"   "NOIR_1"  "ORF76"  
## [15] "ORF64_1"
## [1] 15

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1    ORF4 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1    ORF5 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1    ORF9 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF38 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF50 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       1   ORF63 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 15:       1 ORF65_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 16:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 17:       1   ORF69 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 18:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 19:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 20:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 21:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 22:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24:       2    ORF6 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2   ORF12 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2   ORF13 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF15 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       2   ORF16 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 32:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 33:       2   ORF23 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 34:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 35:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 36:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 37:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 38:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 39:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 40:       2   ORF39 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 41:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 42:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 43:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 44:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 45:       2   ORF46 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 46:       2   ORF52 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 47:       2   ORF54 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 48:       2   ORF58 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 49:       2   ORF60 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 50:       2   ORF62 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 51:       2   ORF68 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 52:       2   ORF71 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 53:       2   ORF72 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 54:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 55:       3    ORF7 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 56:       3   ORF24 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 57:       3   ORF27 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 58:       3   ORF28 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 59:       3   ORF32 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 60:       3   ORF35 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 61:       3   ORF44 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 62:       3   ORF45 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 63:       3   ORF49 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 64:       3   ORF56 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 65:       3   ORF57 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 66:       3   ORF59 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 67:       3  NOIR_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 68:       3   ORF76 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 69:       4   ORF17 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 70:       4   ORF30 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 71:       4   ORF53 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 72:       5   ORF19 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 73:       5   ORF37 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 74:       5   ORF51 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 75:       5   ORF55 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 76:       5 ORF66_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 77:       6   ORF41 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 78:       6   ORF48 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 79:       7 ORF64_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.59026662
##  2: 0.002173813 -2.3786533 0.5530091 0.59026662
##  3: 0.002173813 -2.3786533 0.5530091 0.59026662
##  4: 0.002173813 -2.3786533 0.5530091 0.59026662
##  5: 0.002173813 -2.3786533 0.5530091 0.59026662
##  6: 0.002173813 -2.3786533 0.5530091 0.59026662
##  7: 0.002173813 -2.3786533 0.5530091 0.59026662
##  8: 0.002173813 -2.3786533 0.5530091 0.59026662
##  9: 0.002173813 -2.3786533 0.5530091 0.59026662
## 10: 0.002173813 -2.3786533 0.5530091 0.59026662
## 11: 0.002173813 -2.3786533 0.5530091 0.59026662
## 12: 0.002173813 -2.3786533 0.5530091 0.59026662
## 13: 0.002173813 -2.3786533 0.5530091 0.59026662
## 14: 0.002173813 -2.3786533 0.5530091 0.59026662
## 15: 0.002173813 -2.3786533 0.5530091 0.59026662
## 16: 0.002173813 -2.3786533 0.5530091 0.59026662
## 17: 0.002173813 -2.3786533 0.5530091 0.59026662
## 18: 0.002173813 -2.3786533 0.5530091 0.59026662
## 19: 0.002173813 -2.3786533 0.5530091 0.59026662
## 20: 0.002173813 -2.3786533 0.5530091 0.59026662
## 21: 0.002173813 -2.3786533 0.5530091 0.59026662
## 22: 0.002630562 -1.9748104 0.3778197 0.20208360
## 23: 0.002630562 -1.9748104 0.3778197 0.20208360
## 24: 0.002630562 -1.9748104 0.3778197 0.20208360
## 25: 0.002630562 -1.9748104 0.3778197 0.20208360
## 26: 0.002630562 -1.9748104 0.3778197 0.20208360
## 27: 0.002630562 -1.9748104 0.3778197 0.20208360
## 28: 0.002630562 -1.9748104 0.3778197 0.20208360
## 29: 0.002630562 -1.9748104 0.3778197 0.20208360
## 30: 0.002630562 -1.9748104 0.3778197 0.20208360
## 31: 0.002630562 -1.9748104 0.3778197 0.20208360
## 32: 0.002630562 -1.9748104 0.3778197 0.20208360
## 33: 0.002630562 -1.9748104 0.3778197 0.20208360
## 34: 0.002630562 -1.9748104 0.3778197 0.20208360
## 35: 0.002630562 -1.9748104 0.3778197 0.20208360
## 36: 0.002630562 -1.9748104 0.3778197 0.20208360
## 37: 0.002630562 -1.9748104 0.3778197 0.20208360
## 38: 0.002630562 -1.9748104 0.3778197 0.20208360
## 39: 0.002630562 -1.9748104 0.3778197 0.20208360
## 40: 0.002630562 -1.9748104 0.3778197 0.20208360
## 41: 0.002630562 -1.9748104 0.3778197 0.20208360
## 42: 0.002630562 -1.9748104 0.3778197 0.20208360
## 43: 0.002630562 -1.9748104 0.3778197 0.20208360
## 44: 0.002630562 -1.9748104 0.3778197 0.20208360
## 45: 0.002630562 -1.9748104 0.3778197 0.20208360
## 46: 0.002630562 -1.9748104 0.3778197 0.20208360
## 47: 0.002630562 -1.9748104 0.3778197 0.20208360
## 48: 0.002630562 -1.9748104 0.3778197 0.20208360
## 49: 0.002630562 -1.9748104 0.3778197 0.20208360
## 50: 0.002630562 -1.9748104 0.3778197 0.20208360
## 51: 0.002630562 -1.9748104 0.3778197 0.20208360
## 52: 0.002630562 -1.9748104 0.3778197 0.20208360
## 53: 0.002630562 -1.9748104 0.3778197 0.20208360
## 54: 0.002630562 -1.9748104 0.3778197 0.20208360
## 55: 0.005127433 -0.5566122 0.2345080 0.82739367
## 56: 0.005127433 -0.5566122 0.2345080 0.82739367
## 57: 0.005127433 -0.5566122 0.2345080 0.82739367
## 58: 0.005127433 -0.5566122 0.2345080 0.82739367
## 59: 0.005127433 -0.5566122 0.2345080 0.82739367
## 60: 0.005127433 -0.5566122 0.2345080 0.82739367
## 61: 0.005127433 -0.5566122 0.2345080 0.82739367
## 62: 0.005127433 -0.5566122 0.2345080 0.82739367
## 63: 0.005127433 -0.5566122 0.2345080 0.82739367
## 64: 0.005127433 -0.5566122 0.2345080 0.82739367
## 65: 0.005127433 -0.5566122 0.2345080 0.82739367
## 66: 0.005127433 -0.5566122 0.2345080 0.82739367
## 67: 0.005127433 -0.5566122 0.2345080 0.82739367
## 68: 0.005127433 -0.5566122 0.2345080 0.82739367
## 69: 0.005224449 -1.2350532 1.5108478 0.06845455
## 70: 0.005224449 -1.2350532 1.5108478 0.06845455
## 71: 0.005224449 -1.2350532 1.5108478 0.06845455
## 72: 0.002585386 -1.9080987 0.3087534 0.43210279
## 73: 0.002585386 -1.9080987 0.3087534 0.43210279
## 74: 0.002585386 -1.9080987 0.3087534 0.43210279
## 75: 0.002585386 -1.9080987 0.3087534 0.43210279
## 76: 0.002585386 -1.9080987 0.3087534 0.43210279
## 77: 0.004830169 -0.9381876 0.3682901 0.16904056
## 78: 0.004830169 -0.9381876 0.3682901 0.16904056
## 79: 0.005278328 -1.0831543 0.8420568 0.12160986
##           se.bp          v         c       pchi

## [1] "ORF63" "ORF74"
## [1] 2
##  [1] "ORF7"   "ORF24"  "ORF27"  "ORF28"  "ORF32"  "ORF35"  "ORF44"  "ORF45" 
##  [9] "ORF49"  "ORF56"  "ORF57"  "ORF59"  "NOIR_1" "ORF76"  "ORF41"  "ORF48"
## [1] 16

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       3    ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32:       3    ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33:       3    ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34:       3   ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35:       3   ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36:       3   ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37:       3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38:       3   ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39:       4    ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40:       4   ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41:       4   ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42:       4   ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43:       4   ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44:       4   ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45:       4   ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46:       4   ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47:       4   ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48:       4   ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49:       4   ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50:       4   ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51:       4   ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52:       4   ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53:       4   ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54:       4   ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55:       5    ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56:       5   ORF24 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57:       5   ORF27 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58:       5   ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59:       5   ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60:       5   ORF35 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61:       5   ORF44 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62:       5   ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 63:       5   ORF49 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 64:       5   ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 65:       5   ORF57 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 66:       5   ORF59 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 67:       5  NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 68:       5   ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 69:       6   ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 70:       6   ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 71:       6   ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 72:       7   ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 73:       7   ORF37 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 74:       7   ORF51 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 75:       7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 76:       8   ORF41 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 77:       8   ORF48 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 78:       9   ORF55 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 79:      10 ORF64_1 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.590266623
##  2: 0.002173813 -2.3786533 0.5530091 0.590266623
##  3: 0.002173813 -2.3786533 0.5530091 0.590266623
##  4: 0.002173813 -2.3786533 0.5530091 0.590266623
##  5: 0.002173813 -2.3786533 0.5530091 0.590266623
##  6: 0.002173813 -2.3786533 0.5530091 0.590266623
##  7: 0.002173813 -2.3786533 0.5530091 0.590266623
##  8: 0.002173813 -2.3786533 0.5530091 0.590266623
##  9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.002585386 -1.9080987 0.3087534 0.432102790
## 63: 0.002585386 -1.9080987 0.3087534 0.432102790
## 64: 0.002585386 -1.9080987 0.3087534 0.432102790
## 65: 0.002585386 -1.9080987 0.3087534 0.432102790
## 66: 0.002585386 -1.9080987 0.3087534 0.432102790
## 67: 0.002585386 -1.9080987 0.3087534 0.432102790
## 68: 0.002585386 -1.9080987 0.3087534 0.432102790
## 69: 0.004830169 -0.9381876 0.3682901 0.169040559
## 70: 0.004830169 -0.9381876 0.3682901 0.169040559
## 71: 0.004830169 -0.9381876 0.3682901 0.169040559
## 72: 0.005278328 -1.0831543 0.8420568 0.121609856
## 73: 0.005278328 -1.0831543 0.8420568 0.121609856
## 74: 0.005278328 -1.0831543 0.8420568 0.121609856
## 75: 0.005278328 -1.0831543 0.8420568 0.121609856
## 76: 0.005181368 -0.8929713 1.1657673 0.068980610
## 77: 0.005181368 -0.8929713 1.1657673 0.068980610
## 78: 0.005202505 -0.4915675 0.2569468 0.451195188
## 79: 0.005277337 -0.4694357 0.4086000 0.002664175
##           se.bp          v         c        pchi

## [1] "ORF61" "ORF74" "ORF46" "ORF62" "ORF37"
## [1] 5
##  [1] "ORF4"    "ORF5"    "ORF9"    "ORF38"   "ORF50"   "ORF63"   "ORF65_1"
##  [8] "ORF69"   "ORF17"   "ORF30"   "ORF53"   "ORF55"   "ORF64_1"
## [1] 13

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       3    ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32:       3    ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33:       3    ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34:       3   ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35:       3   ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36:       3   ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37:       3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38:       3   ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39:       4    ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40:       4   ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41:       4   ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42:       4   ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43:       4   ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44:       4   ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45:       4   ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46:       4   ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47:       4   ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48:       4   ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49:       4   ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50:       4   ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51:       4   ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52:       4   ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53:       4   ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54:       4   ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55:       5    ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56:       5   ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57:       5   ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58:       5   ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59:       5   ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60:       5  NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61:       5   ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62:       6   ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 63:       6   ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 64:       6   ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 65:       7   ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 66:       7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 67:       8   ORF24 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 68:       8   ORF27 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 69:       8   ORF35 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 70:       8   ORF44 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 71:       8   ORF49 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 72:       8   ORF57 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 73:       8   ORF59 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 74:       9   ORF37 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 75:       9   ORF51 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 76:      10   ORF41 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 77:      10   ORF48 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 78:      11   ORF55 0.6118917 0.8437067 0.6974597 0.033505179 0.0189981734
## 79:      12 ORF64_1 0.5880849 0.8219482 0.7195606 0.034578844 0.0209653160
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.590266623
##  2: 0.002173813 -2.3786533 0.5530091 0.590266623
##  3: 0.002173813 -2.3786533 0.5530091 0.590266623
##  4: 0.002173813 -2.3786533 0.5530091 0.590266623
##  5: 0.002173813 -2.3786533 0.5530091 0.590266623
##  6: 0.002173813 -2.3786533 0.5530091 0.590266623
##  7: 0.002173813 -2.3786533 0.5530091 0.590266623
##  8: 0.002173813 -2.3786533 0.5530091 0.590266623
##  9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.004830169 -0.9381876 0.3682901 0.169040559
## 63: 0.004830169 -0.9381876 0.3682901 0.169040559
## 64: 0.004830169 -0.9381876 0.3682901 0.169040559
## 65: 0.005278328 -1.0831543 0.8420568 0.121609856
## 66: 0.005278328 -1.0831543 0.8420568 0.121609856
## 67: 0.005181368 -0.8929713 1.1657673 0.068980610
## 68: 0.005181368 -0.8929713 1.1657673 0.068980610
## 69: 0.005181368 -0.8929713 1.1657673 0.068980610
## 70: 0.005181368 -0.8929713 1.1657673 0.068980610
## 71: 0.005181368 -0.8929713 1.1657673 0.068980610
## 72: 0.005181368 -0.8929713 1.1657673 0.068980610
## 73: 0.005181368 -0.8929713 1.1657673 0.068980610
## 74: 0.005202505 -0.4915675 0.2569468 0.451195188
## 75: 0.005202505 -0.4915675 0.2569468 0.451195188
## 76: 0.005277337 -0.4694357 0.4086000 0.002664175
## 77: 0.005277337 -0.4694357 0.4086000 0.002664175
## 78: 0.004895109 -0.7634588 0.2463505 0.018100690
## 79: 0.004790086 -0.7521758 0.1706391 0.701623569
##           se.bp          v         c        pchi

## [1] "ORF61" "ORF74" "ORF46" "ORF62"
## [1] 4
##  [1] "ORF4"    "ORF5"    "ORF9"    "ORF38"   "ORF50"   "ORF63"   "ORF65_1"
##  [8] "ORF69"   "ORF17"   "ORF30"   "ORF53"   "ORF37"   "ORF51"   "ORF41"  
## [15] "ORF48"   "ORF55"   "ORF64_1"
## [1] 17

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  2:       1   ORF10 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  3:       1   ORF18 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  4:       1   ORF20 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  5:       1   ORF21 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  6:       1   ORF31 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  7:       1   ORF34 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  8:       1   ORF61 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
##  9:       1 ORF67_1 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 10:       1   ORF70 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 11:       1   ORF74 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 12:       1   ORF75 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 13:       1  NOIR_2 0.9941896 0.9983142 0.9660481 0.002112503 0.0007251022
## 14:       2    ORF2 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 15:       2    ORF3 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 16:       2    ORF8 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 17:       2   ORF11 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 18:       2   ORF14 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 19:       2   ORF22 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 20:       2   ORF25 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 21:       2   ORF26 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 22:       2   ORF29 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 23:       2   ORF33 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 24:       2 ORF35.5 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 25:       2   ORF36 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 26:       2     CTO 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 27:       2   ORF40 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 28:       2   ORF42 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 29:       2   ORF43 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 30:       2   ORF73 0.9735798 0.9906794 0.9448661 0.006812226 0.0028963952
## 31:       3    ORF4 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 32:       3    ORF5 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 33:       3    ORF9 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 34:       3   ORF38 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 35:       3   ORF50 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 36:       3   ORF63 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 37:       3 ORF65_1 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 38:       3   ORF69 0.4735100 0.7855631 0.6263131 0.037526829 0.0226428168
## 39:       4    ORF6 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 40:       4   ORF12 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 41:       4   ORF13 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 42:       4   ORF15 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 43:       4   ORF16 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 44:       4   ORF23 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 45:       4   ORF39 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 46:       4   ORF46 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 47:       4   ORF52 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 48:       4   ORF54 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 49:       4   ORF58 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 50:       4   ORF60 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 51:       4   ORF62 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 52:       4   ORF68 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 53:       4   ORF71 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 54:       4   ORF72 0.9538743 0.9969828 0.3913529 0.008460561 0.0007978858
## 55:       5    ORF7 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 56:       5   ORF28 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 57:       5   ORF32 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 58:       5   ORF45 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 59:       5   ORF56 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 60:       5  NOIR_1 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 61:       5   ORF76 0.9648411 0.9866834 0.9451281 0.008569668 0.0039154288
## 62:       6   ORF17 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 63:       6   ORF30 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 64:       6   ORF53 0.7314414 0.9043049 0.7156264 0.027787889 0.0135937819
## 65:       7   ORF19 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 66:       7 ORF66_1 0.8644100 0.9728985 0.5952602 0.017705755 0.0049286483
## 67:       8   ORF24 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 68:       8   ORF27 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 69:       8   ORF35 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 70:       8   ORF44 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 71:       8   ORF49 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 72:       8   ORF57 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 73:       8   ORF59 0.8378420 0.9802404 0.3925050 0.022110120 0.0039916723
## 74:       9   ORF37 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 75:       9   ORF51 0.4303328 0.7729250 0.5927484 0.038588990 0.0232605134
## 76:      10   ORF41 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 77:      10   ORF48 0.4436059 0.8100378 0.5242550 0.039756929 0.0209024829
## 78:      11   ORF55 0.6118917 0.8437067 0.6974597 0.033505179 0.0189981734
## 79:      12 ORF64_1 0.5880849 0.8219482 0.7195606 0.034578844 0.0209653160
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.002173813 -2.3786533 0.5530091 0.590266623
##  2: 0.002173813 -2.3786533 0.5530091 0.590266623
##  3: 0.002173813 -2.3786533 0.5530091 0.590266623
##  4: 0.002173813 -2.3786533 0.5530091 0.590266623
##  5: 0.002173813 -2.3786533 0.5530091 0.590266623
##  6: 0.002173813 -2.3786533 0.5530091 0.590266623
##  7: 0.002173813 -2.3786533 0.5530091 0.590266623
##  8: 0.002173813 -2.3786533 0.5530091 0.590266623
##  9: 0.002173813 -2.3786533 0.5530091 0.590266623
## 10: 0.002173813 -2.3786533 0.5530091 0.590266623
## 11: 0.002173813 -2.3786533 0.5530091 0.590266623
## 12: 0.002173813 -2.3786533 0.5530091 0.590266623
## 13: 0.002173813 -2.3786533 0.5530091 0.590266623
## 14: 0.002630562 -1.9748104 0.3778197 0.202083600
## 15: 0.002630562 -1.9748104 0.3778197 0.202083600
## 16: 0.002630562 -1.9748104 0.3778197 0.202083600
## 17: 0.002630562 -1.9748104 0.3778197 0.202083600
## 18: 0.002630562 -1.9748104 0.3778197 0.202083600
## 19: 0.002630562 -1.9748104 0.3778197 0.202083600
## 20: 0.002630562 -1.9748104 0.3778197 0.202083600
## 21: 0.002630562 -1.9748104 0.3778197 0.202083600
## 22: 0.002630562 -1.9748104 0.3778197 0.202083600
## 23: 0.002630562 -1.9748104 0.3778197 0.202083600
## 24: 0.002630562 -1.9748104 0.3778197 0.202083600
## 25: 0.002630562 -1.9748104 0.3778197 0.202083600
## 26: 0.002630562 -1.9748104 0.3778197 0.202083600
## 27: 0.002630562 -1.9748104 0.3778197 0.202083600
## 28: 0.002630562 -1.9748104 0.3778197 0.202083600
## 29: 0.002630562 -1.9748104 0.3778197 0.202083600
## 30: 0.002630562 -1.9748104 0.3778197 0.202083600
## 31: 0.005127433 -0.5566122 0.2345080 0.827393673
## 32: 0.005127433 -0.5566122 0.2345080 0.827393673
## 33: 0.005127433 -0.5566122 0.2345080 0.827393673
## 34: 0.005127433 -0.5566122 0.2345080 0.827393673
## 35: 0.005127433 -0.5566122 0.2345080 0.827393673
## 36: 0.005127433 -0.5566122 0.2345080 0.827393673
## 37: 0.005127433 -0.5566122 0.2345080 0.827393673
## 38: 0.005127433 -0.5566122 0.2345080 0.827393673
## 39: 0.005224449 -1.2350532 1.5108478 0.068454546
## 40: 0.005224449 -1.2350532 1.5108478 0.068454546
## 41: 0.005224449 -1.2350532 1.5108478 0.068454546
## 42: 0.005224449 -1.2350532 1.5108478 0.068454546
## 43: 0.005224449 -1.2350532 1.5108478 0.068454546
## 44: 0.005224449 -1.2350532 1.5108478 0.068454546
## 45: 0.005224449 -1.2350532 1.5108478 0.068454546
## 46: 0.005224449 -1.2350532 1.5108478 0.068454546
## 47: 0.005224449 -1.2350532 1.5108478 0.068454546
## 48: 0.005224449 -1.2350532 1.5108478 0.068454546
## 49: 0.005224449 -1.2350532 1.5108478 0.068454546
## 50: 0.005224449 -1.2350532 1.5108478 0.068454546
## 51: 0.005224449 -1.2350532 1.5108478 0.068454546
## 52: 0.005224449 -1.2350532 1.5108478 0.068454546
## 53: 0.005224449 -1.2350532 1.5108478 0.068454546
## 54: 0.005224449 -1.2350532 1.5108478 0.068454546
## 55: 0.002585386 -1.9080987 0.3087534 0.432102790
## 56: 0.002585386 -1.9080987 0.3087534 0.432102790
## 57: 0.002585386 -1.9080987 0.3087534 0.432102790
## 58: 0.002585386 -1.9080987 0.3087534 0.432102790
## 59: 0.002585386 -1.9080987 0.3087534 0.432102790
## 60: 0.002585386 -1.9080987 0.3087534 0.432102790
## 61: 0.002585386 -1.9080987 0.3087534 0.432102790
## 62: 0.004830169 -0.9381876 0.3682901 0.169040559
## 63: 0.004830169 -0.9381876 0.3682901 0.169040559
## 64: 0.004830169 -0.9381876 0.3682901 0.169040559
## 65: 0.005278328 -1.0831543 0.8420568 0.121609856
## 66: 0.005278328 -1.0831543 0.8420568 0.121609856
## 67: 0.005181368 -0.8929713 1.1657673 0.068980610
## 68: 0.005181368 -0.8929713 1.1657673 0.068980610
## 69: 0.005181368 -0.8929713 1.1657673 0.068980610
## 70: 0.005181368 -0.8929713 1.1657673 0.068980610
## 71: 0.005181368 -0.8929713 1.1657673 0.068980610
## 72: 0.005181368 -0.8929713 1.1657673 0.068980610
## 73: 0.005181368 -0.8929713 1.1657673 0.068980610
## 74: 0.005202505 -0.4915675 0.2569468 0.451195188
## 75: 0.005202505 -0.4915675 0.2569468 0.451195188
## 76: 0.005277337 -0.4694357 0.4086000 0.002664175
## 77: 0.005277337 -0.4694357 0.4086000 0.002664175
## 78: 0.004895109 -0.7634588 0.2463505 0.018100690
## 79: 0.004790086 -0.7521758 0.1706391 0.701623569
##           se.bp          v         c        pchi

## [1] "ORF61" "ORF74" "ORF46" "ORF62"
## [1] 4
##  [1] "ORF4"    "ORF5"    "ORF9"    "ORF38"   "ORF50"   "ORF63"   "ORF65_1"
##  [8] "ORF69"   "ORF17"   "ORF30"   "ORF53"   "ORF37"   "ORF51"   "ORF41"  
## [15] "ORF48"   "ORF55"   "ORF64_1"
## [1] 17

Remove genes from clusters ?

##  [1] "ORF4"    "ORF5"    "ORF9"    "ORF38"   "ORF50"   "ORF63"   "ORF65_1"
##  [8] "ORF69"   "ORF17"   "ORF30"   "ORF53"   "ORF37"   "ORF51"   "ORF41"  
## [15] "ORF48"   "ORF55"   "ORF64_1"
## [1] 17
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       2    17
##  2:       4    16
##  3:       1    13
##  4:       3     8
##  5:       5     7
##  6:       8     7
##  7:       6     3
##  8:       7     2
##  9:       9     2
## 10:      10     2
## 11:      11     1
## 12:      12     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters